Follow the Carbon Part 2

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Follow the Carbon (Part 2)

• Lecture 3
• DNA/RNA/CELL

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Nucleic acids (DNA/RNA)

• Deoxyribonucleic acid (DNA), is a nucleic acid
  that contains the (genetic) instructions used in
  the development and functioning of all known
  living organisms.
• Collection of nucleotides linked together in long
  polymers the largest macromolecule

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Nucleotide
Each nucleotide 1) Five-carbon sugar
molecule 2) One or more phosphate groups 3)
Nitrogen-containing compound nitrogenous base
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G
C
T
A
DNA is a string of letters
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Strand
Watson and Crick (1953) realized that DNA have a
double helix.
DNA strand DNA strand A T T A G C C G
Hydrogen bond (weak)
A can link only with T G can link only with C
Two DNA strands are complimentary to each other
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Hydrogen bonds in DNA
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Can you think of any reasons for two DNA strands?
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DNA vs. RNA

• Deoxyribonucleic acid (DNA) deoxyribose sugar
• Ribonucleic acid (RNA) ribose sugar
• Four bases
• DNA RNA
• A adenine A
• G guanine G
• C cytosine C
• T thymine U uracil

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Ribose
Deoxyribose
DNA parts
RNA parts
Thymine
Uracil
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RNA is a single-stranded but not a linear
molecule.The shape is very important for
catalytic purposes
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Three major functions of DNA/RNA

• DNA replication through templated polymerization
• DNA transcription into the RNA
• RNA translation into proteins

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DNA Replication (Templated Polymerization)
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• Helicase (motor protein)
• unzips DNA
• 2) DNA primase (protein)
• makes a short primer
• 3) DNA polymerase (protein)
• builds a new DNA strand using
• Old DNA strand as a template

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Rational for Darwins theory

• DNA replication proceeds with high speed human
  DNA (3-billion-base sequence) can be copied in
  several hours
• Even though DNA replication proceeds with
  incredible accuracy, errors do occur (lt 1 error
  per billion bases copied) mutations.
• If the organism survives the mutation, it will be
  copied every time DNA is replicated
• Mutations cause diversity within species
• Some mutations have no effect, some are lethal
  and in very rare occasions mutations are useful
  basis for evolution

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Transcription synthesis of RNA under the
direction of DNA
A gene is defined as the segment of DNA sequence
corresponding to a single protein (or to a
single catalytic or structural RNA molecule for
those genes that produce RNA but not protein).
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RNA types

• mRNA messenger RNA (mRNA) RNA molecule that
  specifies the amino acid sequence of a protein.
• rRNA ribosomal RNA (rRNA) Any one of a number of
  specific RNA molecules that form part of the
  structure of a ribosome and participate in the
  synthesis of proteins
• tRNA transfer RNA (tRNA) Set of small RNA
  molecules used in protein synthesis as an
  interface (adaptor) between messenger RNA and
  amino acids.

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Translation
1) Each type of tRNA becomes attached at one end
to a specific amino acid, and displays at its
other end a specific sequence of three
nucleotides 2) Ribosome (rRNAs) latches on one
end of the mRNA trundles through it and picks up
tRNAs loaded with amino acids 3) In the ribosome
tRNAs attach to a matching segment of the mRNA.
The amino acids link together to extend the
growing protein chain. tRNAs, without amino
acids, are released
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The cell

• Nucleic acids, proteins, lipids, carbohydrates
  are parts of the living organism but not the
  living organism by themselves.
• Cell is the smallest unit of any living organism
  which can
• Gather raw materials from the environment
• Construct out of them a new cell with a new copy
  of the hereditary information

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• A small bag of molecules that is separated from
  the outside world
• Bag membrane and cell wall
• There are always DNA, cytosol (internal fluid),
  ribosomes and enzyme in the bag.

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1) Most living organisms are single cells 2) In
multicellular organisms (humans) groups of cells
perform specialized functions 3) But in all
cases, whether we discuss the solitary bacterium
or the aggregate of more than 1013 cells (human
body), the whole organism has been generated by
cell divisions from a single cell.
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A few common features of all Cells

• All Cells store their hereditary information in
  the DNA
• All Cells replicate their hereditary information
  by templated polymerization
• All Cells transcribe portions of their hereditary
  information into the same intermediary form (RNA)
• All Cells use proteins as catalysts

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• First question of Astrobiology
• How does life begin and evolve?
• We know that
• a) Life requires carbon-based macromolecules
  lipids, proteins, carbohydrates, nucleic acids.
• b) Life has the smallest living units cells.
• Two approaches to the origin of life
• biological Top-down strategy
• chemical Bottom-up strategy

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Two Approaches to the origin of life

• Top-down strategy is to
• look at the present day biology
• and extrapolate back towards
• the simplest living entities.
• Bottom-up strategy is to make
• the complex building blocks of life
• (organic macromolecules) and put
• them together.

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Top-down strategy What are the minimum
requirements on the number of genes?

• The smallest known genomethe bacterium
  Mycoplasma genitalium. (parasite in mammals). It
  has only 477 genes in its genome of 580,070
  nucleotide pairs.
• Does it mean that Mycoplasma genitalium is the
  most ancient bacterium?
• The minimum number of genes for a viable cell in
  today's environments is probably no less than
  200300.
• Nakabachi A, Yamashita A, Toh H, Ishikawa H,
  Dunbar H, Moran N, Hattori M (2006). "The
  160-kilobase genome of the bacterial endosymbiont
  Carsonella.". Science 314 (5797) 267

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Top-down strategy How would the most ancient
cell look like?

• Cells are very diverse in size, shape and
  complexity but there are 2 basic cell types
• Prokaryotes are much simpler and smaller than
  eukaryotes
• Eukaryotes have a cell nucleus (to protect DNA)
  while prokaryotes do not
• Prokaryotes are single-celled only
• Eukaryotes may be either single-celled or
  multicellular

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Prokaryotes
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Eukaryotic cell
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Eukaryotes vs. Prokaryotes

• Who outnumbers and outweighs the other?
• Who is more dependent on the other?

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Eukaryotes look much more complex then
prokaryotes. Do we see the difference in the DNA
structure? Yes
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• Is the genome (order of nucleotides) of
  Eukaryotes and Prokaryotes completely different?
  No
• Some parts of the genome change more easily than
  others in the course of evolution
• A segment of the DNA responsible for coding of
  ribosomal parts (16S RNA, 1500 nucleotides) is
  very well conserved.

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• A part of the gene for 16S RNA (1500
  nucleotides) for different organisms.
• Corresponding segments of nucleotide sequence
  from an archaean (Methanococcus jannaschii), a
  eubacterium (Escherichia coli) and a eucaryote
  (Homo sapiens) are aligned in parallel.
• Sites where the nucleotides are identical between
  species are indicated by a vertical line.
• Genetic information conserved since the
  beginnings of life.

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Top-down strategyThe Tree of Life

• By looking at the changes in 16S RNA we can
  identify three domains of life Bacteria, Archaea,
  and Eucaryotes

Prokaryotes
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Problems with DNA/RNA/protein world

• DNA has information to reproduce itself but needs
  proteins to catalyze the reaction
• Proteins can catalyze reactions but cant
• reproduce by themselves
• It is very unlikely that all DNA/RNA/proteins
  components
• would form spontaneously at the same time.

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RNA World Hypothesis

• RNA is an information carrier (like DNA)
• RNA molecules can act as catalysts (unlike DNA)
• But self-replicating systems of RNA molecules
  have not been found in nature yet

Origin of Life
RNA world
DNA/protein world